Despite hundreds of sequentered arabidopsis genomes, very few things are known about the degree of genomic collinearity within a single species due to the low number of assemblies at the chromosome level. Here we report assemblies of reference quality at the seven Arabidopsis Thaliana chromosome level selected on its global range. Each genome reveals between 13 and 17 Mb rearranged and 5 to 6 MB of reference sequences introducing copy number modifications in approximately 5,000 genes, including ~ 1900 non-reference genes.
Quantify the collinearity between the genomes reveals ~ 350 euchromatic regions, where tandem duplications specific to adhesion destroy collinearity between genomes. These hot spots of rearrangements are characterized by reduced meiotic recombination in the hybrids and genes involved in the biotic stress response. This suggests that hot spots of rearrangements undergo a modified evolutionary dynamic, compared to the rest of the genome, which are mainly based on the accumulation of new mutations and not on the recombinant of existing variation and thus allow a quick response to biotic stress.
Gene duplication is a major mechanism for the evolution of the novelty of genes and the copy number variation is a major contribution to interindividual genetic diversity. However, most approaches to study the variation-copy number rely on a single mapping reads a genome reference and are not able to distinguish duplicate sequences. Specialized approaches to interrogate specific paralogues are relatively slow and have a high degree of computing complexity, limiting their effective application to emerging population data sets. We present Quick-Mer2, an autonomous and mapping approach that allows the rapid construction of the para-specific copying numbers of the short playback sequence data.
This approach is based on the tabulation of unique k-sea sequences from short reading datasets and is capable of analyzing a 20x coverage human genome in about 20 min. We applied our recently published sequence data approach from the Genomes 1000 project, built paralogical copy numbers of 2457 unrelated persons and a variation of copy numbers discovery of paralogual genes. We identify nine genes where none of the analyzed samples has a number of two, 92 genes where the majority of the samples has a copy number other than two and describe a rare copy number variation that performs several genes on the locus. APOBEC3.
Isolation of intact chloroplast to sequence plastid genomes of five species of Festuca.
The isolation of good quality chloroplast DNA (CPDNA) is a challenge in different species of plants, although several isolation methods are known. Attempts have been undertaken to isolate CPDNA of Festuca’s grass species using standard protocols available; However, they failed due to difficulties in the separation of intact chloroplasts of polysaccharides, oleoresin and contaminated nuclear DNA in gross homogenate.
In this study, we present a fast and inexpensive protocol to isolate intact chloroplasts of seven grass varieties / addresses of five species of Festuca using a single 30% solution of PERCOLL. This protocol has managed to isolate high quality CPDNA with the slightest contamination of the other DNA. We performed the Illumina Misseq Keaked-End sequencing (2 × 300 bp) using 200 ng of CPDNA of each variety / adhesion.
The mapping of the chloroplast genome showed that 0.28% -11.37% were chloroplast readings, which covered 94% to 96% of the reference plastid genomes of tightly linked grass species. This improved method provided a high quality CPDNA of seven grass varieties / addresses of five species of Festuca and could be useful for other grass species with a similar genome complexity.
Simple method improved for the identification of mycobacteria by Maldi-tof MS (laser desorption mass spectrometry assisted by the matrix).
The purpose of this study was to establish a simple method for the rapid identification of malcobacterial species of Maldi-tof (matrix-assisted laser desorption / ionization time of the flight mass spectrometry) using the Biotype Biotype System Maldi-tof (Bruker Daltonik, Bremen, Germany). A multicenter, prospective and unique study was carried out in three European hospitals, two Spanish hospitals and a British from May to August 2018. The BD BCACTEC MGIT liquid culture system (Becton Dickinson, Berks, UK) was used in the three centers for the growth of mycobacteria. When the positive signal, tubes have been removed from the analyzer and, in addition to the standard laboratory procedures, have been enduiling on blood agency plates for Maldi-tof analysis.
The plates were incubated aerobically for 1 to 7 days at 37 ° C and inspected every day. Once any growth was visible, it has been transferred to the steel target plate, superimposed with 1 μl of neat formic acid and a 1 μL HCCA matrix (alpha-hydroxyl 4 cinnamic acid) and analyzed in a Biotype Bruker Maldi. -TOF. The results given by Maldi-tof have been compared to the reference methods used for identification in the different centers.
In two Spanish hospitals, the identification of Maldi-tof was only attempted on presumed non-tuberculosis Mycobacteria (NTM) and the results were initially compared to the results obtained by a commercial reverse hybridization dosage, genotype cm / Like (Hain Lifescience, Tübingen, Germany). At the British Hospital, the identification of all presumptive mycobacteria was attempted and compared to the results obtained by complete genome sequencing (WGS). Overall in 142/167 (85%) of cases, the identifications obtained were concordant; All Isolates of Mycobacterium Tuberculosis (MTB) 43/43 (100%), 57/76 (75%) of mycobacteria rapid growth (NTM) and 42/48 (85%) Slow growth in NTM growth tested has been correctly identified.
We report a new, easy, cheap and fast isolation and identification of Mycobacterium spp. Without the need for additional steps or equipment and this method is used in the routine used in the three centers.